Later that year, Arlene attempted to prevent Agent Scully from entering Skinner's office while Scully was attempting to receive help for her partner, Agent Mulder, who had become lost at sea in the Bermuda Triangle. Scully was able to surpass Arlene and barge into Skinner's office. (TXF: "Triangle")

In 1999, AD Skinner was admitted to a hospital after being infected with nanobots by Alex Krycek. When trying to recall events that had occurred previously, he remembered saying, "Good morning," to Arlene. (TXF: "S.R. 819")

Shortly after, Arlene interrupted a meeting conducted by AD Skinner and AgentArnold upon discovering that Agent Mulder was involved in a hostage situation at the Cradock Marine Bank. (TXF: "Monday")

In late 1999, Skinner gave Arlene orders not to allow Agent Scully to enter his office. Arlene once again attempted to persuade Scully not to enter Skinner's office, but failed. Scully ended up saving Skinner from Alex Krycek, and Arlene promptly called an ambulance. (TXF: "The Sixth Extinction II: Amor Fati")

In 2002, Arlene was present when Oliver Martin psychokinetically levitated AD Skinner. She poured him a glass of water, and soon afterward, Martin had a seizure and collapsed on the floor of the office. She reported this activity immediately to AD Skinner. (TXF: "Sunshine Days")